Yuba County Water Agency Yuba River Development Project FERC Project No 2246 Study 3.3 DRAFT SPECIAL-STATUS AMPHIBIANS – FOOTHILL YELLOW-LEGGED FROG SURVEYS March 11February 28, 2010 [This study proposal was discussed at the 3/10 Relicensing Participants meeting The redlined changes below were made by Licensee based on that meeting, and Amy Lind said agencies/NGOs would redline the study proposal by 4/14/10 Besides other things, Amy will consider including surveying for crayfish as was included in the Pit 3, and Management Plan, and adding a trigger for a focused surveys in a second year as Phase II of the study JML 3/11] 1.0 Project Nexus Yuba County Water Agency’s (YCWA or Licensee) continued operation and maintenance (O&M) of the Yuba River Development Project (Project) has a potential to affect the specialstatus1 amphibian, foothill yellow-legged frog (FYLF) (Rana boylii), which is considered a State Species of Special Concern by the California Department of Fish and Game (CDFG) 2.0 Resource Management Goals of Agencies with Jurisdiction Over the Resource to be Studied [Agencies – Section 5.11(d)(2) states that an applicant for a new license must in its proposed study “Address any known resource management goals of the agencies or Indian tribes with jurisdiction over the resource to be studied.” If each agency provides to YCWA a brief written description of their jurisdiction over the resource to be addressed in this study, YCWA will insert the brief description here/or attach it stating the description was provided by that agency If not, prior to issuing the PAD, YCWA will describe to the best of its knowledge and understanding the management goals of each agency that YCWA believes has jurisdiction over the resource addressed in this study Licensee] 3.0 Study Goals and Objectives The goal of this study is to develop information concerning the special-status amphibians associated with Project-affected stream reaches, and related Project recreation features or activities The specific objectives of this study are as follows: Special-status amphibians are considered those species: 1) found on National Forest System land and formally listed by the United States Department of Agriculture Forest Service as a Sensitive Species or a Management Indicator Species; 2) listed under the federal Endangered Species Act (ESA) as Proposed or a Candidate for listing as endangered or threatened or proposed for delisting; 3) listed under the California Endangered Species Act (CESA) as Proposed for listing as endangered or threatened or proposed for delisting; or 5) formally listed by California Department of Fish and Game as a Species of Concern For the purpose of this study proposal, species listed as threatened or endangered under the ESA or CESA are addressed separately Draft – 3/1/102/28/10 Pre-Application Document ©2010, Yuba County Water Agency FYLF Surveys Page of 11 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 • Identify, compile, and map known occurrences of FYLF, including life history stage and associated habitat information as available At a minimum, produce a map of known occurrences with a supplemental table that includes information on the exact location, date found, how many individuals (if available), and the source of the sighting (museum database, agency record, etc.) • Identify habitats in the study area potentially suitable for FYLF, and evaluate the suitability of these habitats for the species • Perform biological surveys in suitable habitats and determine approximate period in which breeding and rearing occurs if FYLF is found • Compile incidental observations from other aquatic studies documenting other native amphibians, and non-native aquatic species that may affect the distribution of FYLF 4.0 Existing Information and Need for Additional Information Existing and relevant information regarding known and potentially occurring locations of special-status amphibians in the Project Vicinity2 are available from California Natural Diversity Database (CNDDB), museum records, and other sources FYLF is the only special-status amphibian in the area Information and a life history description of FYLF, included in Section 7.3 of Licensee’s Preliminary Information Package (YCWA 2009), is useful in identifying preferred habitats and documenting where the species have been found to date Table 4.0-1 summarizes habitat requirements of FYLF by life stage Table 4.0-1 Foothill yellow-legged frog habitat requirements by life stage Egg Masses1 Larvae1 Egg masses are deposited in low to Generally in low velocity segments of moderate gradient streams, usually within streams, such as edgewater habitat shallow, edgewater areas of low velocity adjacent to riffles or cascades, in main with cobble/boulder substrate in open, channel pools, and plunge-pools that sunny areas with little riparian vegetation; provide escape cover (e.g., substrate often adjacent to low gradient interstices, vegetation, and detritus for cobble/boulder bars, tributary confluences, cover) Larvae, at least in early stages, side and backwater pools, or pool tail-outs show affinity to oviposition sites, but may with coarse substrates In small streams disperse to shallow, warm, low velocity may occur in step pools and other near-shore habitats with smaller substrate microhabitats that meet basic conditions for (i.e., gravel/sand) as the season substrate, water depth, and velocity progresses Sources of information: Jennings and Hayes 1994, PG&E 2001, Lind 2005 Juveniles and Adults1 Perennial streams and ephemeral creeks with pools Prefer areas that provide exposed basking sites and cool shady areas adjacent to water’s edge Shallow, flowing water, preferentially in small to moderate-sized streams with some cobble-sized substrate FYLF is a stream-adapted species and is not associated with ponds, lakes, or other lentic habitats Within large streams, FYLF often occurs near tributaries, which may provide important seasonal For the purposes of the Relicensing, the Project Vicinity is defined as the area surrounding the Project in the order of a county or United States Geological Survey 1:24,000 topographic quadrangle FYLF Surveys Page of 11 Pre-Application Document ©2010, Yuba County Water Agency Draft – 3/11/102/28/10 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 habitats (e.g., in winter and during the hottest part of the summer) (VanWagner 1996; Seltenrich and Pool 2001) Breeding tends to occur in spring or early summer and eggs are laid in areas of shallow, slow moving, waters near the shore FYLF are infrequent in habitats where introduced fish and American bullfrog occur (Jennings et al 1994) The CNDDB (CDFG 2003) reports 24 occurrences of FYLF in the Project Vicinity The records cited by Vindum and Koo (1999) for the drainages of the North, Middle, and South Yuba rivers occur above Project-affected reaches California Academy of Sciences (2010) has 17 FYLF records from Sierra County, seven from Yuba County, and six from Nevada County The Museum of Vertebrate Zoology has nine specimens from Yuba County Despite widespread documentation of FYLF in the region, none of these records are from the Project Area During stream habitat mapping in 2009, Licensee observed FYLF in Oregon Creek and in Middle Yuba River downstream of Our House Diversion Dam In most cases, existing information is too general to meet the objectives of the study Additional information needed includes specific and current localities of each of the species and their habitats in relation to Project facilities; and sufficient information on normal Project O&M activities that might affect populations 5.0 Study Methods and Analysis 5.1 Study Area The study area consists of stream reaches affected by the Project; it also includes tributaries unaffected by the Project up to 0.5 mile (mi) upstream from the normal high water line of Project-affected stream reaches, if suitable habitat for FYLF is accessible to the species from habitat in the mainstem of the river This includes: 1) the Middle Yuba River from and including Our House Diversion Dam Impoundment to the confluence with the North Yuba River, 2) Oregon Creek from and including the Log Cabin Diversion Dam Impoundment to the confluence with the Middle Yuba River, 3) the North Yuba River from and including New Bullards Bar Dam Reservoir to the confluence with the Middle Yuba River, and 4) the portion of the Yuba River from the confluence of the North and Middle Yuba rivers to New Colgate Powerhouse The Yuba River below New Colgate Powerhouse is below 600 feet (ft) in elevation and thus outside of the known or expected distribution of FYLF, which extends from about 600 ft to 5,000 ft in elevation (Moyle 1973, Seltenrich and Pool 2002, ECORP Consulting, Inc 2005) In addition, the study area includes tributaries up to 1.0 mile (mi) upstream of New Bullards Bar Reservoir, Our House Diversion Dam Impoundment and Log Cabin Diversion Dam Impoundment if suitable habitat is accessible to the species from habitat in the reservoirs and impoundments FYLF may make seasonal movements between tributaries and mainstem streams For the purposes of this document, the Project Area is defined as the area within the existing Federal Energy Regulatory Commission (FERC) existing Project Boundary and the land immediately surrounding the FERC Project Boundary (i.e., within about 0.25 mile of the FERC Project Boundary) and includes Project-affected reaches between facilities and downstream to the next major water controlling feature or structure Draft – 3/1/102/28/10 Pre-Application Document ©2010, Yuba County Water Agency FYLF Surveys Page of 11 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 If YCWA proposes an addition to the Project, the study area will be expanded if necessary to include areas potentially affected by the addition 5.2 General Concepts and Procedures The following general concepts and practices apply to the study: • Personal safety is the most important consideration of each fieldwork team • Licensee will make a good faith effort to obtain permission to access private property where needed well in advance of entering the property • Field crews may make minor variances to the FERC-approved study in the field to accommodate actual field conditions and unforeseen problems When minor variances are made, Licensee’s field crew will follow the protocols in the FERC-approved study • When Licensee becomes aware of major variances to the FERC-approved study, Licensee will issue an e-mail to the Relicensing Contact List describing the variance and reason for the variance Licensee will contact by phone the Forest Service (if the variance is on National Forest System land), USFWS, SWRCB and CDFG to provide an opportunity for input regarding how to address the variance Licensee will issue an e-mail to the Relicensing Contact List advising them of the resolution of the variance Licensee will summarize in the final study report all variances and resolutions • Licensee’s performance of the study does not presume that Licensee is responsible in whole or in part for measures that may arise from the study • Global Positioning System (GPS) data will be collected using either a Map Grade Trimble GPS (sub-meter data collection accuracy under ideal conditions), a Recreation Grade Garmin GPS unit (3 meter data collection accuracy under ideal conditions), or similar units GPS data will be post-processed and exported from the GPS unit into Geographic Information System (GIS) compatible file format in an appropriate coordinate system using desktop software The resulting GIS file will then be reviewed by both field staff and Licensee’s relicensing GIS analyst Metadata will be developed for deliverable GIS data sets • Licensee will provide training to field crews to identify [agencies to develop a short suggested standard species list to be included here in each study proposal assuming Licensee agrees with the list – Licensee 4/15/10] that may reasonably be encountered coincidently during the performance of this study Training will include instructions in diagnostic features and habitat associations of the above species Field crews will also be provided laminate identification sheets showing the above species compared to other common species that may be encountered All incidental observations will be reported in the appropriate Licensee report (e.g., incidental observations of special-status fish recorded during fieldwork for the Special-Status Turtles – Western Pond Turtle Study will be reported in Licensee’s Stream Fish Populations Study report) The purpose of this effort is not to conduct a focus study (no effort in addition the specific field tasks identified for the specific study) or to make all field crews experts in identifying all species, but only to opportunistically gather data during the performance of the study FYLF Surveys Page of 11 Pre-Application Document ©2010, Yuba County Water Agency Draft – 3/11/102/28/10 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 • Field crews will be trained on and provided with materials (e.g Quat or bleach) for decontaminating their boots, waders, and other equipment between study sites Major concerns are amphibian chytrid fungus, and invasive invertebrates (e.g Zebra mussels) This is of primary importance when moving: (1) between tributaries and mainstem reaches, moving between basins (e.g Upper Middle Yuba, Lower Yuba, North Yuba), and (3) moving between isolated wetlands or ponds and river or stream environments 5.3 Study Methods The study will be completed in five steps, each of which is described below 5.3.1 Step – Map Occurrences Licensee will map known occurrences of FYLF based on a query of the CNDDB, agency records, museum records, and consultation with regional experts The map will be supplemented with a table that includes information on the exact location, date found, how many individuals (if available), and the source of the sighting (museum database, agency record, etc.) 5.3.2 Step - Identify Potential Habitat and Select Survey Sites Licensee will review available data sources to identify areas of potentially suitable habitat for FYLF (emphasizing potential breeding habitat) based on the description of habitat elements presented in Table 4.0-1 Data sources may include aerial photographs; the Project helicopter video, National Wetland Inventory (NWI) maps, United States Geological Survey (USGS) 1:24,000 topographic quadrangle, hydrologic data, and other sources of information that would allow for assessment of habitat conditions within the study area Licensee may conduct a field reconnaissance at specific locations to assess on-site habitat conditions if other data sources are not adequate to this purpose Sites will be logged by GPS position, photographs will be taken of each site from various angles, and a preliminary habitat assessment will be conducted Pertinent habitat characteristics to be recorded will include stream channel form and dimensions, gradient, substrate types, and vegetation types (e.g., aquatic, emergent, overhanging, and canopy) Following review of habitat data sources, a representative set of sites determined to be potentially suitable habitat or all sites, if few suitable sites are identified, will be selected for surveys Evaluation of potential survey sites will be conducted collaboratively with the relicensing participants The selection of survey sites will take into account site-specific conditions, including safety, accessibility (i.e., road or trail access, topography), permission from landowners to survey on private lands, and potential impact from Project O&M To the extent reasonable, FYLF survey sites will be co-located with other relicensing study sites In addition to the project affected reaches, survey work will be conducted on the unimpaired North Yuba River or another collaboratively agreed upon unimpaired river The results of these surveys will provide context (reference conditions) for evaluating the results of surveys in the project-affected reaches Draft – 3/1/102/28/10 Pre-Application Document ©2010, Yuba County Water Agency FYLF Surveys Page of 11 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 Licensee will invite interested and available Relicensing Participants into the field to comment on the final selection of survey sites 5.3.3 Step – Conduct Surveys Surveys for FYLF will occur during the breeding season and will follow the VES standard protocols developed by Pacific Gas & Electric Company (PG&E) for hydroelectric project applications (Seltenrich and Pool 2002, PG&E and NID 2009) Specifically, two surveyors working in tandem will search both stream banks, back channel areas, and potential instream habitats for FYLF walking slowly while one observer scans ahead Habitats along each bank will be searched To aid in the detection of eggs and larvae, surveyors will use a viewing box in shallow margin areas In water too deep to survey by wading, or where substrate configuration (e.g., large boulders) or other factors render the viewing box ineffective, snorkeling will be employed in appropriate habitats during searches where safely accessible Each FYLF detection will be recorded by life stage along with the associated habitat data based on procedures described in Seltenrich and Pool 2002 Three FYLF VES visits will be conducted; two visits in the spring/early summer for the detection of eggs and early tadpoles, and one in the late summer/early fall to detect older tadpoles and recently metamorphosed frogs Following the initial VES, surveyors will complete a habitat characterization of each study location, following standard operating procedures Prior to conducting the surveys, Licensee will obtain necessary CDFG scientific collection permits and will adhere to accepted decontamination guidelines to minimize the likelihood of transmitting diseases (USFWS 2005) Invasive bullfrogs (Lithobates [Rana] catesbeianus) and crayfish are known predators of FYLF If these species are seen during FYLF VES, additional focused surveys should be conducted to determine their extent/distribution, relative abundance, and lifestage distribution within project reaches VES methods for FYLF can be adapted for bullfrog surveys in lotic waters For crayfish, PG&E’s Pit3,4,5 FYLF monitoring plan provides examples of methods for counting 5.3.4 Step – Prepare, Format and Quality Assurance/Quality Control Data Following field surveys, Licensee will develop GIS maps depicting special-status species occurrences, potential habitat, project facilities and features, and other information collected during the study Field data will then be subject to quality assurance and quality control (QA/QC) procedures, including spot-checks of transcription and comparison of GIS maps with field notes 5.3.5 Step – Prepare Report Licensee will prepare a report that includes the following sections: 1) Study Goals and Objectives; 2) Methods and Analysis; 3) Results; 4) Discussion; and 5) Description of Variances FYLF Surveys Page of 11 Pre-Application Document ©2010, Yuba County Water Agency Draft – 3/11/102/28/10 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 from the FERC-approved study proposal, if any At a minimum, the following summaries/data presentations will be provided, along with the supporting data (in Excel spreadsheet and GIS layers, as appropriate): • Presence/absence of FYLF by survey period (e.g., spring, summer), sample reach tributary, and river • Abundance of FYLF egg masses by survey period, sample reach tributary, and river • Abundance of FYLF tadpoles/tadpole groups by survey period, sample reach tributary, and river • Abundance of FYLF young of the year (metamorphs), subadults, and adults by survey period, sample reach tributary, and river • Descriptive summaries of FYLF egg mass and tadpole habitat characteristics (at least n, mean, minimum, maximum, and standard error values) overall and by river and/or tributary • Summary and maps of site habitat assessments For all special-status species observations, Licensee will complete the appropriate CNDDB form and transmit the form to the CNDDB 5.3.6 Step – Consultation and Evaluating Need for Focused Studies (Second Year) If the results of the study not provide sufficient information for analyses, Licensee will collaborate with Relicensing Participants to determine if additional limited scope studies are needed For example, if the study documents only post-metamorphic life stages of FYLF (adult, juvenile, or young-of-year) or if only late stage larvae are detected (i.e., the results not indicate where FYLF breeding occurred), further focused survey for egg masses and/or early tadpoles in the same stream may be appropriate These are only examples, and other conditions or circumstances may indicate a need for other focused studies of a particular site If Licensee and Relicensing Participants collaboratively agree a second year of focused studies is appropriate, Licensee and Relicensing Participants will collaboratively develop a new study proposal and Licensee will file it with FERC and implement the study 6.0 Study-Specific Consultation Licensee will engage in the following study-specific consultation: • Licensee will invite interested and available Relicensing Participants into the field to comment on the final selection of study sites • Licensee will collaborate with Relicensing Participants regarding need for focused second year studies as discussed in Step Draft – 3/1/102/28/10 Pre-Application Document ©2010, Yuba County Water Agency FYLF Surveys Page of 11 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 7.0 Schedule Licensee anticipates the schedule to complete the study as follows assuming the PAD is filed on November 1, 2010, and FERC issues its Study Determination by October 4, 2011: Identify Habitat and Select Survey Sites (Step 1) October 2011 – March 2012 Conduct Surveys (Step 2) March 2012 – August 2012 QA/QC (Step 3) .September 2012 Report Preparation (Step 4) September 2012 - October 2012 8.0 Consistency of Methodology with Generally Accepted Scientific Practices This study is consistent with the goals, objectives, and methods outlined for recent FERC hydroelectric relicensing efforts in California, and uses well established data from CDFG and other reputable sources for the analysis 9.0 Level of Effort and Cost [Relicensing Participants – Licensee will include a cost range estimate for this study in its Proposed Study Plan Licensee] 9.0 References Cited California Academy of Sciences (CAS) 2010 Herpetology Records Online: http://www.calacademy.org/research/herpetology/catalog/Index.asp (Accessed January 21, 2010) CDFG (California Department of Fish and Game) 2003 Biogeographic Data Branch California Natural Diversity Database (CNDDB) Version 3.1.0-Dated January 4, 2010 Online at: http://www.dfg.ca.gov/bdb/html/cnddb.html (Accessed January 20, 2010) ECORP Consulting, Inc 2005 Draft results of the 2004 (Year 1) amphibian monitoring program for foothill yellow-legged frog and mountain yellow-legged frog El Dorado Hydroelectric Project (FERC Project No 184) Report to El Dorado Irrigation District May 18, 2005 Jennings, M R., and M P Hayes 1994 Amphibian and reptile species of special concern in California Final Report to the California Department of Fish and Game, Inland Fisheries Division, Rancho Cordova, CA 225 pp Lind, A 2005 Reintroduction of a declining amphibian: determining an ecologically feasible approach for the foothill yellow-legged frog (Rana boylii) through analysis of decline FYLF Surveys Page of 11 Pre-Application Document ©2010, Yuba County Water Agency Draft – 3/11/102/28/10 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 factors, genetic structure, and habitat associations Ph.D Dissertation, University of California, Davis 169 pp Moyle, P.B 1973 Effect of introduced bullfrogs, Rana catesbeiana, on the native frogs of the San Joaquin Valley, California Copeia 1973:18-22 Museum of Vertebrate Zoology (MVZ) 2010 Herpetological records for Yuba, Sierra, and Nevada counties, California University of California, Berkeley – Online http://mvzarctos.berkeley.edu/SpecimenSearch.cfm (Accessed January 21, 2010) PG&E (Pacific Gas and Electric Company) 2001 Survey protocols, standard operating procedures, and data sheets for amphibian surveys and habitat assessments May 2001 Unpublished PG&E and NID (Nevada Irrigation District) 2009 Study 2.3.6 Foothill Yellow-Legged Frog Surveys Study Revised Study Plan, Drum Spaulding Project and Yuba Bear Hydroelectric Project Seltenrich, C P and A C Pool 2002 A standardized approach for habitat assessments and visual encounter surveys for the foothill yellow-legged frog (Rana boylii) Pacific Gas and Electric Company USFWS 2005 Revised Guidance on Site Assessments and Field Surveys for the California Red-legged Frog Online: http://www.fws.gov/sacramento/es/documents/crf_survey_guidance_aug2005.doc (Accessed November 2007) Van Wagner, T 1996 Selected life history and ecological aspects of a population of foothill yellow-legged frogs (Rana boylii) from Clear Creek, Nevada City, California Master's Thesis, California State University Chico 143pp Vindum, J.V and M.S Koo 1999 Amphibians and reptiles of the Tahoe National Forest: historical collections and the results of 1997-1999 California Academy of Science Surveys Dept of Herpetology, California Academy of Sciences Yuba County Water Agency (YCWA) 2009 Yuba River Development Project relicensing Preliminary Information Package http://www.ycwa-relicensing.com/default.aspx Draft – 3/1/102/28/10 Pre-Application Document ©2010, Yuba County Water Agency FYLF Surveys Page of 11 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 FYLF Surveys Page 10 of 11 Pre-Application Document ©2010, Yuba County Water Agency Draft – 3/11/102/28/10 Yuba County Water Agency Yuba River Development Project FERC Project No 2246 Page Left Blank Draft – 3/1/102/28/10 Pre-Application Document ©2010, Yuba County Water Agency FYLF Surveys Page 11 of 11 ... locations of special-status amphibians in the Project Vicinity2 are available from California Natural Diversity Database (CNDDB), museum records, and other sources FYLF is the only special-status. .. observations of special-status fish recorded during fieldwork for the Special-Status Turtles – Western Pond Turtle Study will be reported in Licensee’s Stream Fish Populations Study report) The... example, if the study documents only post-metamorphic life stages of FYLF (adult, juvenile, or young-of-year) or if only late stage larvae are detected (i.e., the results not indicate where FYLF breeding